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Cecilia-Sensalari committed Aug 23, 2021
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -16,7 +16,7 @@ To position ancient WGD events with respect to speciation events in a phylogeny,

*ksrates* is user-friendly command-line tool and [Nextflow](https://github.com/nextflow-io/nextflow) pipeline to compare paralog and ortholog *K*<sub>S</sub> distributions derived from genomic or transcriptomic sequences. *ksrates* estimates differences in synonymous substitution rates among the lineages involved and generates an adjusted mixed plot of paralog and ortholog *K*<sub>S</sub> distributions that allows to assess the relative phylogenetic positioning of presumed WGD and speciation events.

For more details, see our [preprint](https://www.biorxiv.org/content/10.1101/2021.02.28.433234v1) and the documentation below.
For more details, see the related [publication](https://doi.org/10.1093/bioinformatics/btab602) and the documentation below.

## Documentation

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2 changes: 1 addition & 1 deletion doc/source/concept.rst
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Expand Up @@ -9,7 +9,7 @@ However, when the lineages involved exhibit different substitution rates, the va

*ksrates* is an open-source tool offering a rate-adjustment strategy that brings all the distributions to a common *K*:sub:`S` scale by compensating for the differences in synonymous substitution rates relative to the species of interest, the focal species. The final mixed plot produced by *ksrates* features rate-adjusted positions of the ortholog *K*:sub:`S` estimates of species divergence times that help to clarify the phylogenetic placement of WGDs inferred in the focal species.

For more detail about the methodology, please see our `preprint <https://www.biorxiv.org/content/10.1101/2021.02.28.433234v1>`__.
For more detail about the methodology, please see the related `publication <https://doi.org/10.1093/bioinformatics/btab602>`__.


.. _`explained_example`:
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